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What is FACT?
FACT compares the architecture of features such as functional domains,
secondary structure motifs and compositional properties between pairs of
proteins. A feature dotplot (FDP) allows for a rapid and intuitive assessment
to what extent two proteins agree in their feature architecture, and thus may
share a similar function. An automated scoring routine complements the FDP
and is used to search entire proteomes for proteins with potentially similar
function to a given query sequence.

Which features will be annotated?
We annotate the features listed below. Unless otherwise
noted, the programs used for feature prediction are embedded into the SFINX package (Sonnhammer and
Wootton (2001) Protein: Structure, Function, and Genetics 45: 262-273).

How does the similarity scoring work?
FACT calculates the similarity between a query protein and every protein from the chosen search proteome. The similarity is based on the feature architectures of the proteins. Four such scoring schemata are implemented and the scores will be calculated simultanously. Details about the FACT, MS_uni and MS_st scoring will follow soon. The Lib score is a modified version from Lin et. al.(2006 Bioinformatics
22(17):2081-2086).

Example output
To illustrate FACT we have used the human glutathione S-transferase to search for a functionally equivalent protein in the proteome of yeast Saccharomyces cerevisiae. For the query protein and all proteins in the search-proteome the FACT, MS_uni, MS_st and Lin scores will be computed. The sequences from the search-proteome are ranked according to their score. From the resulting list, any pair-wise comparison can be extracted and displayed in the feature dotplot. Finally, a histograms of all FACT scores are displayed.